Is there a function or a way to retrieve the path of root home directory of a shiny app?
The shiny app I run creates multiple directories and changes working directory. But at point in the app, I need to jump to the home directory. getwd() won't work unless I run it first and save it as a variable or something.
I am thinking of something like the below command used to read a file from a package home directory on any platform without knowing the actual path.
#get root dir
system.file()
# read a file from the root dir of a package
a <- system.file("bla",package="foo")
The approach has to work locally, on shiny-server and shinyapps.io. (In situations where I cannot set the path manually).
Related
First of all I set my working directory as following
setwd("C:/Users/asus/Desktop/App-1")
Then I can call the app with the following code:
runApp("C:/Users/asus/Desktop/App-1")
But I cannot call the app via :
runApp("App-1")
The script in the directory is named as "app.R" but it appears in the directory as "app".
Whereas, in the R webpage it says if I create a new directory named App-1 it should have worked. But It does not. Many thanks.
I'm new to 'golem'. So far I did my Shiny apps as packages, with the app in the folder inst/app, and then to use 'shinytest' I made a folder inst/app/shinytest. How to do with 'golem'? There's no app folder: inst/app only contains www, and the UI and the server are some functions in the package.
So I need to know where to put the 'shinytest' script and how to deal with 'testthat' and the expect_pass function? (I don't want to use testServer)
I've found. It suffices to create a file app.R in the app folder with these contents:
mypackage::run_app()
I have a Shiny app that works as expected both locally and when containerized. The app receives some user input, queries a database, and returns a .zip containing a .pdf and .xlsx file. Because reasons, I will be deploying it to a server running Shiny Server. When running the app, I get an error that processing the [filename].knit.md is impossible because "Permission denied:"
After digging into why this might be the case, I think it's a function of the user shiny (running the app in shiny-server.conf) doesn't have permissions to access the dir/file. The trouble I'm having is diagnosing this error because the temp dir and file don't appear to exist anywhere in the local directory structure.
In server.R, I call tempfile() and use that temporary file as the input for output_file in the render() command. I know that tempfile() is a subdirectory of the per-session temporary directory so how can I ensure that user shiny can access any tempdir() created during app operation?
Further, am I assuming correctly that the temp dir in the image above is automatically deleted when the app errors out? I can't find that dir anywhere in the /tmp tree of the server.
In the doc of tempdir()
By default, tmpdir will be the directory given by tempdir(). This will be a subdirectory of the per-session temporary directory found by the following rule when the R session is started. The environment variables TMPDIR, TMP and TEMP are checked in turn and the first found which points to a writable directory is used: if none succeeds ‘/tmp’ is used. The path should not contain spaces. Note that setting any of these environment variables in the R session has no effect on tempdir(): the per-session temporary directory is created before the interpreter is started.
So
mkdir mydir
export TMPDIR=mydir
Rscript -e "tempfile();tempdir();"
give
[1] "mydir/RtmphR2Rkx/file19da392dac5546"
[1] "mydir/RtmphR2Rkx"
Else give the right to /tmp
I have a series of pieces of R code which have been designed to be run on other computers. That is, all code is relative to a root directory, which contains a Rstudio project file, .Rproj. There are no absolute file paths. This works fine when I actually open Rstudio, load the .Rproj file and then run the code.
However some of my code takes hours to run, and I need to set multiple scripts to run one after the other. This means creating a .sh file, and running the R script in turn from the command line. However non of my programs run successfully from the command line, as the root directory is no longer set to that of the .Rproj file. I have read about the here package can be used, which will automatically set the root directory to where ever a .here file is located. This is not the case for me.
The working directory it automatically uses is the home directory I have on the computational cluster I am using. The area where all my files, including the .Rproj and .here files is located in a different directory in which I have a lot more space allocated. Both are accessible from a common parent directory, so I assumed there here() function would be able to locate the directory I want to actually use to run my work. But this is not the case.
Effectively, I would like to set the root directory to a location which is not the default root directory on the system I am using. I have put a .here file there, but this is not located by there here() function, which I believe is its primary objective. Any ideas on how to proceed?
EDIT: I am working on a UNIX system. R version 3.4.2.
My problem was similar, but not exactly the same as yours. Perhaps my solution will work for you. When I opened an RStudio project, I found that if I called "library(here)", the root directory is set where the .Rproj file is located and that "set_here" would not change that directory, despite the 'here' package documentation. Perhaps I was doing something wrong, but I decided to solve the problem with a simple R function that moves up the directory tree until it finds a ".here" file. It then loads the "here" package and that sets the root directory where I want it.
I use "touch .here" in a Terminal outside of R to set my root directory, and then call "init_here()" from my newly opened R project:
init_here <- function() {
`%!in%` = Negate(`%in%`)
files <- dir( all.files = T )
while ( ".here" %!in% files & getwd()!="/" ) {
setwd("..")
files <- dir( all.files = T )
}
library(here)
}
Use Case -
In Unix:
cd( '~/myRoot' )
touch( '.here' )
In RStudio, when I open a project, the calls look like:
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
< R information removed for clarity >
[Workspace loaded from ~/myRoot/myProject/.RData]
> getwd()
[1] "/Users/me/myRoot/myProject"
> init_here()
here() starts at /Users/me/myRoot
> here()
[1] "/Users/me/myRoot"
>
I can now put a ".here" file at the root of each of my RStudio projects and set the expected root directory independently for each project. If you want to get fancy, you could put the function in each project's .Rprofile so that it runs whenever the project is opened. All of my projects have the .Rproj file in the directory above my "R" directory, so my .Rprofile looks like:
source("./R/init_here.R")
init_here()
Hope that helps.
Did you try simply adding a cd /the/path/where/you/put/the/files command in your shell script?
According to this documentation, here() "uses a reasonable heuristics to find your project's files, based on the current working directory at the time when the package is loaded". The "cd" (change directory) command in a shell script changes the current working directory.
I'm using blogdown and Hugo to generate a website.
I've created a new R project and have downloaded the theme using:
blogdown::new_site(dir = "Theme", theme = 'pacollins/hugo-future-imperfect-slim') and I can preview the template once downloaded. However, if I close R and then restart and I use the add-in "serve site" I get the following error message:
Error in site_root(config) :
Could not find config.toml / config.yaml under...
and then the directory that the config.toml file is saved in (and all of the rest of the theme files) are listed.
I can't understand what's changing between being able to preview the site in R Studio Viewer, then quitting R and restarting and it not being able to find the config file.
I did find this advice: https://github.com/rstudio/blogdown/issues/48 which suggests that my working directory is not the root directory of the website. There are two things I don't understand:
1) How can the the root directory and working directory work together okay when I initially download the theme, until I quit R and restart, and then they appear to not be the same?
2) How to I change the root directory of the website to fix the issue?
Thanks!
If you followed the blogdown's documentation to create a new site with the command "blogdown::new_site(dir="/your/website/dir")", it will set your working directory to "/your/website/dir".
When you restart R/Rstudio, your current working directory is reset (probably to your home directory). You can check the current working directory with getwd().
The solution is simply set up the working directory:
The simpler way is to execute setwd("/your/website/dir"), then you should be able to run blogdown::serve_site()
The recommended way is to create a Rstudio project at /your/website/dir with File-New Project-Existing Directory. It will create a .Rproj file under the root directory of your website. After that, you can "open project" and work on your website, then preview with serve_site().